Can a clear line be drawn between academic scholarship and political imperatives? Of all the questions raised by Yale University’s recent closure of the Yale Initiative for the Interdisciplinary Study of Antisemitism (YIISA), this one is the most acute.

Even with the news that Yale is going to replace YIISA with a new program for the study of anti-Semitism, it is still instructive to think about what brought YIISA down. The institute’s detractors essentially fell into two categories. Some, like the bloggers Philip Weiss and Antony Lerman, marked its demise with displays of schadenfreude, having long caricatured YIISA as a Zionist advocacy organization masquerading as an academic institute.

A second group, represented by professor Deborah Lipstadt who wrote last week, was sympathetic to YIISA in its conception, yet critical of its execution. According to this view, YIISA spent too much time agitating against anti-Semitism, especially as manifested in the Muslim world, and not enough time studying the phenomenon dispassionately.

Both these perspectives shared the same assumption. YIISA’s tone, focus, and — as Lerman described it — “politicized approach” toward contemporary anti-Semitism fatally compromised its academic integrity in favor of strident advocacy.

Is that a fair assessment? Take the oft-cited example of YIISA’s bias, the paper delivered to its 2010 conference by Itamar Marcus, the director of the Israeli monitoring organization “Palestinian Media Watch.” Entitled “The Central Role of Palestinian Antisemitism in Creating the Palestinian Identity,” the paper propelled YIISA into the headlines after it sent Maen Areikat, the PLO’s Washington representative, into an apoplectic rage. Arabs were being “demonized” by YIISA, declared Areikat in a letter to Yale President Richard Levin. Since Arabs are “Semites,” he insisted, they cannot be anti-Semitic.

Ironically, Areikat’s reaction underlined just why Marcus’s contribution was supremely pertinent to a conference on anti-Semitism. The “but-we-are-Semites” rationalization frequently heard from Palestinian leaders resonates with ignorant contempt for Jewish history.

The very label ‘anti-Semite’ was coined not by Jews, but by non-Jewish demagogues, who used it to construct an ideology and a political program with mass appeal. When a nation becomes gripped by anti-Semitism, its character changes. Its national identity, malleable by nature, embraces opposition to the Jews as one if its main components: Think of France during Dreyfus, or Germany under the Nazis.

Yet an academic conference which asks whether this is also true of the Palestinian Arabs — whose distinctive identity only crystallized in the context of a violent response to the arrival of the Jewish pioneers — finds itself accused of engaging in political advocacy.

The sad truth is that dead Jews — victims of crusades, pogroms, the Shoah — are safe terrain for academia. Live Jews, however, are a much more daunting proposition.

As anyone connected with YIISA will tell you, the institute’s academic challenge was never about maintaining a studied neutrality. Rather, its staff and fellows had to operate in an academic culture openly in thrall to a set of values that, from the outset, promised confrontation: Hostility toward the idea of Jewish national self-determination, receptiveness toward “Israel Lobby” theories of U.S. Middle East policy, the conceit that anti-Semitism is merely a tool to smear Israel’s opponents.

For that reason, YIISA had to reclaim the anti-Semitism debate. Ultimately, the institute was forced to defend the contention that contemporary anti-Semitism is not a phantom, but a very real social problem.

In that regard, Professor Lipstadt’s own work on Holocaust denial is salient here. In her book on the subject, she argues that her research was essential to prevent deniers from gaining influence as the immediate memory of the Shoah began to fade. In academic parlance, this point of departure would be described as “normative” — we should do x to prevent y — and is no less legitimate because of it.

How was YIISA’s work any different? Its sole offense, I would assert, lay in its determination to go against the grain. Yale may couch its justification for YIISA’s closure in terms of academic standards, but that does nothing to explain the undercurrent of hostility from others on the Yale faculty like Jeffrey Alexander, a professor of sociology, who told NPR: “…it would be as if you had a center for the study of, let’s say, racism, organized by, let’s say, the Black Panther movement.”

If former YIISA director Charles Small is the equivalent of Stokely Carmichael, heaven knows where that leaves Columbia’s tenured anti-Zionist, Joseph Massad, or the London School of Economics, which carried out research funded by the Gadhafi Foundation.

By closing YIISA after only five years, Yale has effectively sided with those voices that demean contemporary anti-Semitism as the fantasy of overzealous Israel advocates. It remains to be seen if the university’s new anti-Semitism program takes up the charge, analyzing anti-Semitism’s all-too-real manifestations, whether in Iran’s state doctrine or on the streets of European cities like Malmo, Leicester and Antwerp. If it doesn’t, we can only hope that Yale’s loss will be another university’s gain.

Ben Cohen is a frequent contributor to the Huffington Post and Pajamas Media and formerly associate director of communications at the American Jewish Committee. Follow him on twitter: @BenCohenOpinion.